[2026-06-08T09:04:23] Launching Arriba 2.4.0
[2026-06-08T09:04:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:04:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:04:35] Reading chimeric alignments from 'aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9528958)
[2026-06-08T09:11:24] Marking multi-mapping alignments (marked=5876640)
[2026-06-08T09:11:29] Detecting strandedness (reverse)
[2026-06-08T09:11:29] Assigning strands to alignments 
[2026-06-08T09:11:31] Annotating alignments 
[2026-06-08T09:12:08] Filtering duplicates (remaining=5335578)
[2026-06-08T09:12:16] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=5093150)
[2026-06-08T09:12:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5093150)
[2026-06-08T09:12:20] Filtering viral contigs with expression lower than the top 5 (remaining=5093150)
[2026-06-08T09:12:26] Filtering viral contigs with less than 5% coverage (remaining=5093150)
[2026-06-08T09:12:28] Estimating fragment length (mate gap mean=-87.3201, mate gap stddev=28.6252, read length mean=132.457)
[2026-06-08T09:12:29] Filtering read-through fragments with a distance <=10000bp (remaining=4770857)
[2026-06-08T09:12:31] Filtering inconsistently clipped mates (remaining=4683153)
[2026-06-08T09:12:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4568512)
[2026-06-08T09:12:38] Filtering fragments with small insert size (remaining=4567797)
[2026-06-08T09:12:40] Filtering alignments with long gaps (remaining=4567796)
[2026-06-08T09:12:42] Filtering fragments with both mates in the same gene (remaining=4566748)
[2026-06-08T09:12:45] Filtering fusions arising from hairpin structures (remaining=4272474)
[2026-06-08T09:12:47] Filtering reads with a mismatch p-value <=0.01 (remaining=2046050)
[2026-06-08T09:13:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=867251)
[2026-06-08T09:13:10] Finding fusions and counting supporting reads (total=644248)
[2026-06-08T09:13:27] Merging adjacent fusion breakpoints (remaining=637944)
[2026-06-08T09:13:28] Filtering multi-mapping fusions by alignment score and read support (remaining=401037)
[2026-06-08T09:14:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=398666)
[2026-06-08T09:14:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=214147)
[2026-06-08T09:14:10] Filtering fusions with <2 supporting reads (remaining=33641)
[2026-06-08T09:14:11] Filtering fusions with an e-value >=0.3 (remaining=10667)
[2026-06-08T09:14:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10716)
[2026-06-08T09:14:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10613)
[2026-06-08T09:14:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10613)
[2026-06-08T09:14:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7573)
[2026-06-08T09:14:22] Searching for fusions with spliced split reads (remaining=7583)
[2026-06-08T09:14:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=4703)
[2026-06-08T09:14:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4635)
[2026-06-08T09:14:28] Searching for fusions with >=4 spliced events (remaining=5432)
[2026-06-08T09:14:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1890)
[2026-06-08T09:14:43] Filtering fusions with anchors <=23nt (remaining=1557)
[2026-06-08T09:14:44] Filtering end-to-end fusions with low support (remaining=1512)
[2026-06-08T09:14:45] Filtering fusions with no coverage around the breakpoints (remaining=1467)
[2026-06-08T09:14:45] Indexing gene sequences 
[2026-06-08T09:14:50] Filtering genes with >=30% identity (remaining=409)
[2026-06-08T09:14:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-08T09:14:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-06-08T09:14:57] Searching for additional isoforms (remaining=208)
[2026-06-08T09:14:59] Assigning confidence scores to events 
[2026-06-08T09:15:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:02] Writing fusions to file 'aih-tih-sc-387c73-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:03] Writing discarded fusions to file 'aih-tih-sc-387c73-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:32] Freeing resources
[2026-06-08T09:15:49] Done (elapsed time=00:11:26, CPU time=00:11:25, peak memory=14.2gb)